The biggest hurdle in success of gene and drug therapy is designing and preparation of suitable bio-nanomaterials to carry the desired nucleic acid and drug to the targeted site. The work described in the present thesis encompasses two different approaches for the delivery of bioactive oligo/polynucleotides and drugs in vitro and in vivo using either cationic lipids or their nanocomposites with different carbon nanomaterials. The idea of using carriers for oligo/polynucleotides and drugs came into existence because of numerous physiological barriers in pathway of delivery of naked oligo/polynucleotides or drugs which reduces the overall activity of these bioactives in biological systems. These barriers trigger scientific research toward the preparation of appropriate biomaterials which can overcome the physiological barriers and improve the activity of bioactive oligo/polynucleotides and drugs in cellular systems. Toward this end, the design and synthesis of different cationic lipids and carbon nanomaterials were undertaken as described in seven chapters of the thesis. A series of novel cationic lipids with structural variability was prepared and used for gene delivery in vitro. They were further tuned chemically to sustain delivery efficiency in high serum percentage during in vitro transfection. These serum compatible lipids were used to perform transfection of reporter gene plasmid and found to be more efficient compared to the some well known commercial products for the same purpose. Another series of novel lipids were synthesized for the targeted gene delivery in vitro. These tryptophan based cholesteryl lipids were used to prepare mixed liposomes. These mixed liposomes were highly efficient in targeting sigma receptor rich HEK293T over sigma receptor negative HeLa cells. Mixed liposomes were also prepared for selective targeting of αvβ3 and αvβ5 integrins in gene transfection protocol using a palmitoyl-RAFT-RGD4 template. A mixed liposomal formulation was developed to carry out anti-sense siRNA mediated knockdown of Smad-2 protein with better efficiency compared to some of the best known commercial products for the same purpose. These mixed liposomes were also highly efficient for regression via induction of p53 mediated apoptosis in xenograft tumors developed in nude mice. Carbon nanomaterials have been extensively explored as nanoscale gene/drug carriers for potential applications. But the challenge is to solubilize these highly hydrophobic materials in aqueous medium for use in biological systems. Although there are reports for covalent modifications of such nanomaterials but it could be done only with the loss of some beneficial features of these materials. Herein a non-covalent technique has been efficiently used to suspend single walled carbon nanotubes in water using biocompatible cationic lipids. These nanosuspensions were used to complex plasmid DNA and transfect them in vitro. They proved to be highly serum compatible DNA carriers which did not drop the efficiency even in very high percentage of serum. Similarly exfoliated graphene was modified with cationic lipid and serum components to improve IC50 of Tamoxifen citrate and Methotrexate to a considerable extent in vitro. The improved Methotrexate formulations were highly efficient for regression in size of xenograft tumors developed in nude mice. Thus, the present thesis entails generation of cationic lipids and carbon nanomaterials based nanocomposites which were not only highly biocompatible themselves but their efficiency was found many fold better compare to some of the best commercial delivery agents. These were useful for the delivery of various bioactive oligo/polynucleotides and drugs in vitro and in vivo.

Récemment, de nombreux efforts ont été consacrés au développement d’oligonucléotides synthétiques pour des applications thérapeutiques et de diagnostique variées. Les oligonucléotides modifiés peuvent inhiber sélectivement l’expression des gènes en se liant spécifiquement à des séquences d’ADN et/ou d’ARN ciblées à travers les stratégies antigène, antisens ou d’ARN interférent. Les aminoxy peptides forment facilement des structures secondaires bien définies comme des alpha-, béta-, gamma-turns ou des hélices, ce qui nous a inspiré pour concevoir de nouveaux oligonucléotides modifiés dans le but d’étudier leurs propriétés physico-chimiques et biologiques. Au cours de ce travail, la synthèse de nucléosides aminoxy acides et de leurs oligomères a été entreprise en séries ribose et désoxyribose. Dans la première partie, les fonctions aminoxyle, acide carboxylique et aldéhyde ont été introduites sur la partie osidique de la thymidine. Différents nucléosides monofonctionnalisés ont été synthétisés à l’aide notamment des réactions de Mitsunobu, d’O-allylation et d’oxydation. Les nucléosides monomères ont ensuite été couplés entre eux conduisant aux nouveaux dinucléosides liés par liaison N-oxy amide, oxime et aminoxy. Dans la seconde partie, la synthèse de différentes uridines aminoxy acides a été étudiée à partir de l’uridine, des 2,2’-anhydro et 2,3’-anhydro uridines. Une uridine aminoxy ester a pu être obtenue en passant par la 3’-oxo uridine via une homologation (réaction de Wittig) et l’introduction de la fonction oxyamine en position 5’ par une substitution nucléophile du dérivé iodé. En parallèle, dans la continuité des travaux réalisés au laboratoire sur la synthèse des glycoamino acides, nous avons synthétisé des C-glycosyl aminoxy acides jamais décrits dans la littérature, dans le but de générer de nouveaux mimes de glycopeptides. A partir du C-allyl glucopyranoside perbenzylé, deux C-glucosyl aminoxy acides diastéréoisomères ont été préparés. / Much recent efforts have been devoted to the development of synthetic oligonucleotides for various therapeutic and diagnostic applications because of their capability to cause selective inhibition of gene expression by bonding to the target DNA/RNA sequences through antigen, antisense and RNA interference. The easy formation of well-defined structures like alpha-, béta-, gamma-turns or helical structures of N-oxy peptides promoted us to design new modified oligonucleotides so as to study their physico-chemical and biological properties. During this work, synthesis of different nucleosides aminoxy acids as well as their oligomers has been investigated. In the first part, aminoxy, carboxylic acid and aldehyde functions were introduced into the sugar ring of thymidine and different monofunctionalized nucleosides were obtained thanks to Mitsunobu, O-allylation and oxidation reactions. Different nucleoside monomers were then linked together, leading to novel dinucleosides with N-oxy amide, oxime or aminoxy linkage. In the second part, preparation of different uridines aminoxy acids was studied by using uridine, 2,2’-anhydro and 2,3’-anhydro uridines as starting materials. An uridine aminoxy ester was obtained from 3’-oxo uridine, through homologation with Wittig reaction and introduction of the oxyamine function by nucleophilic substitution of the 5’-iodo derivative. In parallel, as a continuing program in the laboratory on the glycoamino acids synthesis, we have synthesized novel C-glycosyl aminoxy acids in order to generate new mimes of glycopeptides. From perbenzylated C-allyl glucopyranoside, two diastereomeric C-glucosyl aminoxy acids have been successfully prepared.

Recent experimental studies indicate that polymeric structures with a well-adjusted balance of amphiphilic parts may translocate through self-assembled phospholipid bilayers and enhance the passive trans-membrane transport of smaller molecules. Using a coarse grained lattice Monte Carlo model with explicit solvent we investigate self-assembled lipid bilayers interacting with a linear polymer chain under variation of the hydrophobicity of the chain. Here, we focus on the relationship between the chain's hydrophobicity and its translocation behavior through the membrane as well as induced membrane perturbations. We show, that there is an adsorption transition of the polymer at the bilayer interface, where effectively the solvent phase and the tail phase of the bilayer are equally repulsive for the polymer. Close to this adsorption threshold of the polymer both the translocation probability of the polymer as well as the permeability of the membrane with respect to solvent are enhanced significantly. The frequency of polymer translocation events can be understood quantitatively assuming a simple diffusion along a one-dimensional free energy profile, which is controlled by the effective lipophilicity of the chain and the tail-packing in the bilayer's core. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Indiana University-Purdue University Indianapolis (IUPUI) / Fatty acid elongation is the extension of de novo synthesized fatty acids through a series of four reactions analogous to those of fatty acid synthase. ELOs catalyze the first reaction in the elongation pathway through the condensation of an acyl group with a two carbon unit derived from malonyl-CoA. This study uses the condensing enzyme, EloA, from the cellular slime mold, Dictyostelium discoideum as a model for the family of ELOs. EloA has substrate specificity for monounsaturated and saturated C16 fatty acids and catalyzes the elongation of 16:1Δ9 to 18:1Δ11. Site-directed mutagenesis was used to change residues highly conserved among the ELO family to examine their potential role in the condensation reaction. Mutant EloAs were expressed in yeast and fatty acid methyl esters prepared from total cellular lipids were analyzed by gas chromatography/mass spectrometry. Sixteen out of twenty mutants had a decrease in 18:1Δ11 production when compared to the wild-type EloA with little to no activity observed in ten mutants, four mutants had within 20% of wild-type activity, and six mutants had 10-60% of wild-type activity. Immunoblot studies using anti-EloA serum were used to determine if the differences in elongation activity were related to changes in protein expression for each mutant. Analysis of immunoblots indicated that those mutants with little to no activity, with the exception of T130A and Q203A, had x comparable protein expression to the wild-type. Further research included the solubilization of the His6-ELoA fusion protein and preliminary work toward the isolation of the tagged protein and the use of a radiolabeled condensation assay to determine the activity of the eluted protein. Preliminary results indicated that the protein was solubilized but the eluted protein showed no activity when examined by a condensation assay. The work presented here contributes to a better understanding of the role of certain amino acid residues in the activity of EloA and serves as a stepping-stone for future EloA isolation work.

No description available.

No description available.

Huntington’s disease (HD) and Spinocerebellar ataxia (SCA) are incurable neurodegenerative diseases that affect the central nervous system. Amyloids, highly organized protein aggregates, are a hallmark for many neurodegenerative diseases. The presence and accumulation of amyloids are toxic and constitute the major cause of neuron cell death. Both genetic and environmental factors contribute to the onset and progression of these diseases. However, despite intensive research, the underlying cause remains unclear. The role of viral infection as an environmental factor in the context of neurodegenerative diseases has not received much attention. The purpose of this study is to investigate the effects of Herpes Simplex Virus 1 (HSV-1) infection on nuclear amyloid aggregation in model cell lines of HD and SCA. The research process consists mainly of laboratory work which involved the use of several molecular techniques used in the field of biotechnology. The work comprises cultivating cells, infecting cells with HSV-1, Fluorescence microscopy, Western Blot and isolation and detection of amyloids. Western Blot is used for the analysis of specific proteins associated with protein aggregation in HD and SCA. The techniques used for detecting amyloids are Dot Blot and Antibody-staining of amyloids in cells. The results from Western Blot showed that aggregates changed in the presence of the virus. This pattern is observed for both HD and SCA1 cell lines. A big effort is done in this study to optimize Dot Blot as it is method that could be applied in every lab. Normalization of samples proved to be the most challenging part with Dot Blot. No definitive conclusions can be drawn from the Dot Blot results as reproducibility and sensitivity were lacking. This work addresses some of the difficulties encountered when working with detection of amyloids especially Dot Blot. Antibody-staining of amyloids showed that amyloids were formed in the presence of virus in comparison to non-infected. To conclude, aggregates changed, and amyloids were formed in the presence of virus. These results point to the fact that HSV-1 infection could be involved in the process of nuclear amyloid aggregation. The data presented in this thesis will need further investigation and characterization to identify the precise role of viral-induced amyloid formation in HD and SCA patient cells. / Huntingtons sjukdom (HD) och Spinocerebellära ataxier (SCA) är obotliga neurodegenerativa sjukdomar som påverkar det centrala nervsystemet. Amyloid, proteinaggregat som har en viss konformation är ett kännemärke för många neurodegenerativa sjukdomar. Ackumulering av dessa amyloider är toxiskt och är den främsta orsaken till att nervceller dör. Både genetiska faktorer och miljöfaktorer bidrar till uppkomsten och progressionen av dessa sjukdomar. Trots intensiv forskning är den bakomliggande orsaken emellertid fortfarande oklar. Virusinfektion som en potentiell miljöfaktor har i detta sammanhang inte fått mycket uppmärksamhet. Syftet med denna studie är att undersöka effekterna av Herpes Simplex Virus 1 (HSV-1) infektion på amyloid aggregering i modellcellinjer av HD och SCA. Forskningsarbetet bestod i huvudsakligen av experimentellt arbete med hjälp av flera molekylära tekniker inom bioteknikområdet som cell odling, infektering av celler med HSV-1, fluorescensmikroskopi, Western Blot och isolering och detektion av amyloider. Western Blot användes for att analysera specifika proteiner associerade med protein aggregering i HD och SCA. Amyloider detekterades med Dot Blot och med antikroppar specifika för amyloider. Resultat från Western Blot visade att amyloiderna förändras i virusinfekterade celler. Detta mönster observerades i både HD and SCA1 cellinjer. En stor bemöda görs i denna studie för att optimera Dot Blot eftersom det är en metod som kan användas i alla laboratorier. Normalisering visade sig vara det svåraste med detektion av amyloider. Inga definitiva slutsatser kan dras från dessa experiment, eftersom reproducerbarhet och känslighet var bristande. Detta arbete tar upp några av de svårigheter som uppstod vid arbetande med detektion av amyloider speciellt Dot Blot. Detektion av amyloider med antikropp visade att amyloider bildades till stor utsträckning i infekterade cellinjer i jämförelse med icke-infekterade. Sammanfattningsvis, amyloider förändrades och amyloider bildades i närvaro av virus. Dessa resultat indikerar på att HSV-1 infektion skulle kunna vara involverad i processen av amyloid aggregering. De presenterade uppgifter i detta examensarbete är preliminära och behöver följas upp med ytterligare studier för att identifiera virusens exakta roll i amyloid bildning i HD och SCA patient celler.

[ES] La tesis doctoral "Nanostructured supports for the detection of pathogens and biomolecules of interest based on molecular gates with oligonucleotides" se centra en el diseño de nanomateriales híbridos orgánico-inorgánicos como biosensores innovadores para la detección rápida y específica de patógenos como el virus del papiloma humano (VPH) y la bacteria Vibrio vulnificus, así como biomoléculas relevantes como miR-4732-3p, relacionado con la cardiotoxicidad en pacientes con cáncer. Los sensores desarrollados, basados en puertas moleculares en alúmina mesoporosa y validados con muestras clínicas, destacan por su alta sensibilidad, especificidad, rapidez y facilidad de uso, lo que los hace prometedores para aplicaciones en diagnóstico y monitoreo ambiental. / [CA] The doctoral thesis "Nanostructured supports for the detection of pathogens and biomolecules of interest based on molecular gates with oligonucleotides" focuses on the design of organic-hybrid nanomaterialsInorganic as innovative biosensors for rapid and specific detection of pathogens such as human papillomavirus (HPV) and the bacterium Vibrio vulnificus, as well as relevant biomolecules such as miR-4732-3p, related to cardiotoxicity in cancer patients. The developed sensors, based on mesoporous alumina molecular gates and validated with clinical samples, stand out for their high sensitivity, specificity, speed and ease of use, which makes them promising for applications in diagnosis and environmental monitoring. / [EN] La tesi doctoral "Nanostructured supports for the detection of pathogens and biomolecules of interest based on molecular gates with oligonucleotides" se centra en el disseny de nanomaterials híbrids orgànic-inorgànics com biosensors innovadors per a la detecció ràpida i específica de patògens com el virus del papil·loma humà (VPH) i el bacteri Vibrio vulnificus, així com biomolècules rellevants com miR-4732-3p, relacionat amb la cardiotoxicitat en pacients amb càncer. Els sensors desenrotllats, basats en portes moleculars en alúmina mesoporosa i validats amb mostres clíniques, destaquen per la seua alta sensibilitat, especificitat, rapidesa i facilitat d'ús, la qual cosa els fa prometedors per a aplicacions en diagnòstic i monitoratge ambiental. / This research was supported by project PID2021-126304OB-C41 funded by MCIN/AEI and by European Regional Development Fund - A way of doing Europe. This work has received funding from the European Union’s Horizon 2020 Development of an Innovative Fluorogenic Biosensor for Direct Detection of Vibrio vulnificus, a Climate Change Biomarker research and innovation programme under grant agreement No 899708. This research was also supported by CIBER -Consorcio Centro de Investigación Biomédica en Red (CB06/01/2012), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación. This study forms part of the Advanced Materials programme (MFA/2022/049) and was supported by MCIN with funding from European Union NextGeneration EU (PRTR-C17.I1) and by Generalitat Valenciana. The study was also supported by the grants PID2020-120619RB-I00 funded by MCIN/AEI and CIAICO/2021/293 funded by “Conselleria de Educación, Universidades y Empleo” (Generalitat Valenciana, Spain). / Aranda Sobrino, MDLN. (2024). Nanostructured Supports for Detection of Pathogens and Biomolecules of Interest Based on Molecular Gates with Oligonucleotides [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/211237

Ziel der vorgestellten Arbeit war die Synthese von Nucleolipiden zur Lipophilisierung von Oligonucleotiden sowie deren Untersuchung im Hinblick auf ihre Wechselwirkung und Duplex-Bildung an horizontalen Lipidmembranen und verschiedenen Phasengrenzen zur Entwicklung eines neuartigen Bio-Chips für die RNA/DNA-Analyse. Mit der Synthese N(3)-prenylierter und 2’,3’-O-ketalisierter Pyrimidinbasen Uridin und Methyluridin wurden Nucleolipid-Bausteine dargestellt, die auch als terminale Kopfgruppen eines Oligonucleotid-Dodecamers den lipophilen Charakter dieser Oligonucleotid-Sequenz erhöhten. Für den Einsatz solcher LONs (Lipo-Oligonucleotide) in einer vereinfachten RNA/DNA-Analytik wurde eine Vielzahl von Lipo-Oligonucleotiden mit diversen Nucleolipid-Kopfgruppen synthetisiert und auf ihr Einlagerungsverhalten in künstliche Lipid-Bilayer untersucht. Fluoreszenz-spektroskopische Untersuchungen zeigten, dass alle Lipo-Oligonucleotide in der Lage sind, sich in künstliche Lipid-Bilayer einzulagern. Abhängig von der Struktur, der Länge und der Anzahl der C-Atom-Ketten dieser lipophilen Anker-Bausteine wurden die Geschwindigkeit und die Festigkeit der Verankerung im Lipid-Bilayer beeinflusst. Des Weiteren wurde die Hybridisierung von LONs mit komplementären Oligomeren an Lipidmembranen untersucht. Es konnte gezeigt werden, dass die im Bilayer verankerten Lipo-Oligonucleotide mit komplementären Oligomeren DNA-Duplexe bilden. Die hybridisierte DNA wurde nicht nur über einen kovalent gebundenen Cy5-Fluorophor am Gegenstrang nachgewiesen, sondern auch über den DNA-Interkalator SYBR Green I (SG). Am Beispiel von zwei Lipo-Oligonucleotiden (LON 20 und 23), die sich schnell und fest in der Bilayermembran verankern, konnte eine spontane Akkumulation dieser LONs an CHCl3/H2O sowie H2O/n-Decan Grenzflächen direkt nach der Probenzugabe beobachtet werden. Diese und andere Ergebnisse stützen den Einsatz von Lipo-Oligonucleotiden als Ziel-Oligomere in einem neuartigen RNA/DNA-Nachweisverfahren an Phasengrenzen.